However, i DID NOT follow the instruction to remove the xorg-x11-Mesa-libGL package by

rpm -e --nodeps xorg-x11-Mesa-libGL

Everything seems work fine for me.

However, i am not sure whether this is a correct decision by not removing the xorg-x11-Mesa-libGL. Will it decrease the performance of my 3D application and no over head is cause by this xorg-x11-Mesa-libGL? How can i check whether my 3D driver is working fine?

If you use yum or up2date to upgrade your system, chances are that when a new Mesa package is available it will be installed and the nvidia drivers won't work in 3D until you reinstall the nvidia driver again.
It's no big deal, actually. Open a console and type:

glxinfo

It should show you something like this (meaning: the driver is working fine):